Maybe make Eternal Flower Floette something like Kenya the Spearow: a Pokémon you are supposed to give to another person.Probably for the best to just not code Floette Eternal then, since I find that a waste of data space of something we can’t even obtain at all, including Light of Ruin.
Now that you said it though, the only way we could plausibly obtain Eternal Floette is from another dimension where AZ ended up being killed - or permanently missing, out of that world - and it is unable to find their master since then. Even then, it might cause unfortunate implications if not done carefully, but at least the original Kalos’ own lore remained intact.
That's a good compromise between story and gameplay if you ask me.